Reproduction steps:
1. Create a new project
2. Create any Standard Element (GameObject > UI Toolkit > Standard Elements)
3. Create UI Document
4. Save changes and exit Context mode
5. Drag and drop UXML GameObject to Project window to create a Prefab
6. Expand Prefab dropdown and change Prefab to a different GameObject in the Inspector
7. Observe Hierarchy and Console windows
Actual result: "MissingReferenceException: The object of type 'UnityEngine.UIElements.PanelRenderer' has been destroyed but you are still trying to access it." error is thrown and dropdown with UXML GameObject is still displayed
Expected result: No errors are thrown and all Prefab GameObjects change to the updated Prefab
Reproducible with: 6000.5.0a5, 6000.5.5f1, 6000.6.0b5, 6000.7.0a3
Couldn’t reproduce with: 6000.0.80f1 (No UI Toolkit Hierarchy Integration), 6000.3.20f1, 6000.5.0a3 (No Standard Elements and Panel Renderer)
Reproduced on: Windows 11, macOS Tahoe 26.5 (M4)
Note: Issue is also reproducible with Panel Renderer with source Asset attached and enabled Hierarchy Integration